Contacts of the strand formed by residues 17 - 21 (chain B) in PDB entry 1UZL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 17 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 1.3 68.5 - - - +
18B VAL* 1.3 60.4 + - - +
41B LYS* 3.7 9.2 - - - +
79B GLN* 2.7 36.7 + - - +
80B GLY 2.9 20.0 + - - -
81B PRO 3.2 23.1 + - - -
82B VAL* 3.6 4.2 - - - +
83B GLU* 2.8 38.7 + - - +
84B VAL 3.0 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG 3.7 14.6 - - - +
17B SER* 1.3 75.5 - - - +
19B LEU* 1.3 63.8 + - - +
20B VAL* 3.7 18.4 - - + -
35B LEU* 3.7 27.6 - - + -
40B HIS* 3.7 24.0 - - + +
41B LYS 2.8 12.8 + - - +
42B VAL* 4.0 11.4 - - + -
43B ALA* 2.9 25.5 + - - +
79B GLN* 3.2 9.7 + - - +
82B VAL* 5.0 0.7 - - - -
84B VAL* 3.3 23.6 - - + +
86B VAL* 4.7 2.9 - - + -
225B ALA* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER 4.2 0.2 + - - -
18B VAL* 1.3 74.4 - - - +
20B VAL* 1.3 66.0 + - - +
21B THR* 4.7 3.6 - - + +
43B ALA* 3.4 22.9 - - + +
44B VAL 4.1 2.7 - - - +
45B THR* 3.9 30.3 - - + -
71B ALA* 5.5 1.3 - - + -
72B PHE* 3.9 37.9 - - + +
75B VAL* 3.9 24.0 - - + -
82B VAL* 4.0 23.3 - - + +
84B VAL 2.8 9.9 + - - +
85B LEU* 3.6 9.8 - - + +
86B VAL* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.7 20.2 - - + -
19B LEU* 1.3 77.6 - - - +
21B THR* 1.3 60.1 + - - +
23B GLY* 3.5 9.5 + - - -
28B GLY 3.8 21.3 - - - +
31B ILE* 4.4 4.0 - - + -
32B ALA* 4.2 9.4 - - - -
35B LEU* 4.3 4.5 - - + -
42B VAL* 4.2 12.6 - - + -
43B ALA 2.9 10.0 + - - +
44B VAL* 3.2 10.8 - - + -
45B THR 3.1 19.8 + - - -
86B VAL* 3.5 18.4 - - + -
88B ASN* 3.2 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.7 4.3 - - + -
20B VAL* 1.3 69.4 - - - +
22B GLY* 1.3 63.6 + - - +
45B THR* 3.2 23.1 - - + +
60B CYS* 6.6 0.2 - - - -
62B VAL* 4.6 11.2 - - + +
85B LEU* 4.3 13.9 - - + -
86B VAL 2.9 11.1 + - - +
87B SER* 3.4 6.6 + - - -
88B ASN* 2.1 68.9 + - - +
119B VAL* 4.1 26.2 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il